Well this is not an easy job because your Header & Footer must be common for all pages.
1. Create multiple logo snippet from back end in to header.liquid & Footer.liquid.
2. Manage logos via JS or in Liquid code condition as per your requirement.
If you want any help related this feel free to connect with me.
I think you are using multiple header templates for all pages. I this case it is difficult to manage, Just use multiple logo Images for all template in single header.
Only use required Image with condition on required template.
yes that's right. I know there are easier ways but I'm actually happy I got that far. I don't know how to write the conditions for using multiple logo images for all templates in a single header and footer :(